A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
- Pipeline version
- v1.0.0
- Contact E-mail
- qtl7@cdc.gov
- Project Type
- HMAS tripod analysis
Report generated on 2024-09-06, 20:07 EDT based on data in:
/scicomp/groups-pure/OID/NCEZID/DFWED/EDLB/projects/CIMS/HMAS_pilot/tripod/dev/multiqc_config.yaml/scicomp/groups-pure/OID/NCEZID/DFWED/EDLB/projects/CIMS/HMAS_pilot/tripod/dev/work/65/5386724d91e397811962977001e534
quast_report
Assembly Statistics using Quast.
| Sample Name | N50 (Kbp) | # of contigs >= 1Kbp | Largest contig (Kbp) | Length (Kbp) |
|---|---|---|---|---|
| CIMS-MN-055-SH-M-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-055-SH-K-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-051-IW-M-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-051-IW-K-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-053-SH-K-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-068-IW-M-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-053-IW-K-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-068-IW-K-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-069-SH-K-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-058-SH-K-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-050-IW-M-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-056-IW-M-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-050-SH-M-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-056-IW-K-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-065-IW-M-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-069-IW-K-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-064-IW-M-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-069-SH-M-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-065-SH-M-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-056-SH-K-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-049-SH-K-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-049-IW-K-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-049-SH-M-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-070-SH-K-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-070-IW-K-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-062-SH-M-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-062-IW-K-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-057-IW-M-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-054-SH-K-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
| CIMS-MN-061-IW-K-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-061-IW-M-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-059-IW-K-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-051-SH-K-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-058-IW-K-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-064-SH-M-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-051-SH-M-E_assembled | 433.3 | 21 | 947.7 | 4663.0 |
| CIMS-MN-058-SH-M-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-058-IW-M-E_assembled | 561.2 | 21 | 815.6 | 4714.6 |
| CIMS-MN-065-SH-K-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-064-IW-K-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-063-SH-K-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-053-IW-M-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-057-SH-M-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-057-IW-K-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-054-SH-M-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
| CIMS-MN-060-SH-K-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-068-SH-M-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-055-IW-K-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-064-SH-K-E_assembled | 479.0 | 23 | 938.4 | 4738.6 |
| CIMS-MN-070-SH-M-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-049-IW-M-E_assembled | 496.7 | 25 | 1462.3 | 4788.4 |
| CIMS-MN-063-SH-M-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-060-IW-M-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-070-IW-M-E_assembled | 370.5 | 25 | 1076.6 | 4685.7 |
| CIMS-MN-067-IW-M-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-062-SH-K-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-054-IW-M-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
| CIMS-MN-060-IW-K-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-059-SH-K-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-059-IW-M-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-062-IW-M-E_assembled | 479.2 | 21 | 1508.5 | 4705.7 |
| CIMS-MN-056-SH-M-E_assembled | 434.4 | 23 | 651.0 | 4823.7 |
| CIMS-MN-063-IW-K-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-061-SH-M-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-055-IW-M-E_assembled | 282.8 | 49 | 821.2 | 5038.7 |
| CIMS-MN-059-SH-M-E_assembled | 490.5 | 20 | 1508.5 | 4705.4 |
| CIMS-MN-067-IW-K-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-060-SH-M-E_assembled | 376.8 | 32 | 591.0 | 4916.5 |
| CIMS-MN-050-SH-K-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-053-SH-M-E_assembled | 490.5 | 21 | 1508.5 | 4738.2 |
| CIMS-MN-065-IW-K-E_assembled | 762.6 | 17 | 2005.4 | 4712.3 |
| CIMS-MN-069-IW-M-E_assembled | 729.1 | 23 | 1284.5 | 4937.2 |
| CIMS-MN-067-SH-K-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-067-SH-M-E_assembled | 490.3 | 20 | 1508.5 | 4702.8 |
| CIMS-MN-050-IW-K-E_assembled | 146.8 | 63 | 396.3 | 5187.5 |
| CIMS-MN-068-SH-K-E_assembled | 186.0 | 59 | 514.5 | 5045.0 |
| CIMS-MN-063-IW-M-E_assembled | 762.6 | 15 | 2004.8 | 4711.1 |
| CIMS-MN-057-SH-K-E_assembled | 440.5 | 25 | 1195.4 | 4655.9 |
| CIMS-MN-061-SH-K-E_assembled | 320.2 | 44 | 820.8 | 4896.5 |
| CIMS-MN-054-IW-K-E_assembled | 396.0 | 27 | 659.2 | 4660.0 |
tripod report
Combined summary statistics for all the samples in the run, primer pairs (out of total 2461 in the Salmonella HMAS primer panel).
| Sample Name | # of FP | # of not ident seqs | # of matched most abund. seqs | % of matched most abund. seqs |
|---|---|---|---|---|
| CIMS-MN-056-SH-M-N-MN-M05688-240322 | 9 | 40 | 301 / 350 | 0.860 |
| CIMS-MN-052-SH-M-N-MN-M05688-240322 | 4 | 0 | 0 / 4 | 0.000 |
| CIMS-MN-049-SH-M-N-MN-M05688-240322 | 2 | 57 | 5 / 64 | 0.078 |
| CIMS-MN-056-SH-K-N-MN-M05688-240322 | 18 | 48 | 561 / 627 | 0.895 |
| CIMS-MN-050-SH-M-N-MN-M05688-240322 | 1 | 33 | 0 / 34 | 0.000 |
| CIMS-MN-049-SH-K-N-MN-M05688-240322 | 1 | 70 | 14 / 85 | 0.165 |
| CIMS-MN-059-SH-K-N-MN-M05688-240322 | 24 | 33 | 686 / 743 | 0.923 |
| CIMS-MN-054-SH-K-N-MN-M05688-240322 | 106 | 42 | 2163 / 2311 | 0.936 |
| CIMS-MN-058-SH-K-N-MN-M05688-240322 | 115 | 23 | 2194 / 2332 | 0.941 |
| CIMS-MN-052-SH-K-N-MN-M05688-240322 | 7 | 0 | 0 / 7 | 0.000 |
| CIMS-MN-053-SH-K-N-MN-M05688-240322 | 109 | 22 | 2260 / 2391 | 0.945 |
| CIMS-MN-054-SH-M-N-MN-M05688-240322 | 111 | 54 | 2223 / 2388 | 0.931 |
| CIMS-MN-058-SH-M-N-MN-M05688-240322 | 114 | 20 | 2223 / 2357 | 0.943 |
| CIMS-MN-057-SH-K-N-MN-M05688-240322 | 27 | 83 | 832 / 942 | 0.883 |
| CIMS-MN-050-SH-K-N-MN-M05688-240322 | 3 | 46 | 2 / 51 | 0.039 |
| CIMS-MN-059-SH-M-N-MN-M05688-240322 | 20 | 26 | 441 / 487 | 0.906 |
| CIMS-MN-061-SH-K-N-MN-M05688-240322 | 4 | 40 | 110 / 154 | 0.714 |
| CIMS-MN-060-SH-M-N-MN-M05688-240322 | 0 | 0 | 1 / 1 | 1.000 |
| CIMS-MN-064-SH-K-N-MN-M05688-240322 | 103 | 43 | 2148 / 2294 | 0.936 |
| CIMS-MN-062-SH-M-N-MN-M05688-240322 | 49 | 94 | 1227 / 1370 | 0.896 |
| CIMS-MN-065-SH-K-N-MN-M05688-240322 | 34 | 28 | 965 / 1027 | 0.940 |
| CIMS-MN-057-SH-M-N-MN-M05688-240322 | 25 | 50 | 670 / 745 | 0.899 |
| CIMS-MN-061-SH-M-N-MN-M05688-240322 | 4 | 42 | 68 / 114 | 0.596 |
| CIMS-MN-053-SH-M-N-MN-M05688-240322 | 110 | 20 | 2274 / 2404 | 0.946 |
| CIMS-MN-065-SH-M-N-MN-M05688-240322 | 58 | 38 | 1473 / 1569 | 0.939 |
| CIMS-MN-060-SH-K-N-MN-M05688-240322 | 110 | 16 | 2288 / 2414 | 0.948 |
| CIMS-MN-062-SH-K-N-MN-M05688-240322 | 25 | 61 | 444 / 530 | 0.838 |
| CIMS-MN-068-SH-K-N-MN-M05688-240322 | 39 | 63 | 1012 / 1114 | 0.908 |
| CIMS-MN-076-MN-M05688-240322 | 1 | 0 | 0 / 1 | 0.000 |
| CIMS-MN-066-SH-K-N-MN-M05688-240322 | 2350 | 0 | 0 / 2350 | 0.000 |
| CIMS-MN-070-SH-K-N-MN-M05688-240322 | 59 | 51 | 1485 / 1595 | 0.931 |
| CIMS-MN-051-SH-K-N-MN-M05688-240322 | 115 | 14 | 2305 / 2434 | 0.947 |
| CIMS-MN-068-SH-M-N-MN-M05688-240322 | 62 | 55 | 1599 / 1716 | 0.932 |
| CIMS-MN-064-SH-M-N-MN-M05688-240322 | 112 | 33 | 2286 / 2431 | 0.940 |
| CIMS-MN-051-SH-M-N-MN-M05688-240322 | 116 | 15 | 2305 / 2436 | 0.946 |
| CIMS-MN-066-SH-M-N-MN-M05688-240322 | 2366 | 0 | 0 / 2366 | 0.000 |
| CIMS-MN-075-SH-K-N-MN-M05688-240322 | 6 | 0 | 0 / 6 | 0.000 |
| CIMS-MN-070-SH-M-N-MN-M05688-240322 | 95 | 60 | 2041 / 2196 | 0.929 |
| CIMS-MN-067-SH-K-N-MN-M05688-240322 | 112 | 18 | 2271 / 2401 | 0.946 |
| CIMS-MN-067-SH-M-N-MN-M05688-240322 | 112 | 19 | 2299 / 2430 | 0.946 |
| CIMS-MN-069-SH-K-N-MN-M05688-240322 | 118 | 20 | 2284 / 2422 | 0.943 |
| CIMS-MN-069-SH-M-N-MN-M05688-240322 | 118 | 19 | 2299 / 2436 | 0.944 |
| CIMS-MN-055-SH-M-N-MN-M05688-240322 | 113 | 16 | 2319 / 2448 | 0.947 |
| CIMS-MN-063-SH-M-N-MN-M05688-240322 | 114 | 17 | 2317 / 2448 | 0.946 |
| CIMS-MN-063-SH-K-N-MN-M05688-240322 | 113 | 20 | 2314 / 2447 | 0.946 |
| CIMS-MN-055-SH-K-N-MN-M05688-240322 | 114 | 16 | 2318 / 2448 | 0.947 |
| CIMS-MN-078-IH-MN-M05688-240322 | 2452 | 0 | 0 / 2452 | 0.000 |